Switch style check to Black, prep for 0.8 release (#27)

Author: standage

.gitignore

@@ -6,3 +6,4 @@ build/
 sandbox/
 default.profraw
 .DS_Store
+.vscode/

CHANGELOG.md

@@ -2,6 +2,21 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.8] 2022-08-30
+
+## Changed
+- Updated doctest for `pytaxonkit.list` to include taxa that are updated in the NCBI taxonomy DB less frequently (#13, #14, #21, #24)
+- Other occasional updates to compensate for changes in the NCBI taxonomy DB (#15, #16, #17, #23, #26)
+- Updated `pytaxonkit.list_ranks()` to match updated `taxonkit filter --list-order` behavior (#20)
+- Now using Black instead of pycodestyle to check and autoformat Python code (#27)
+
+### Fixed
+- Bug with how certain functions handle empty inputs (#19)
+- Bug causing `pytaxonkit.lineage` to fail when only a single taxid was provided as input (#22)
+- Bug causing `pytaxonkit.lca` to fail when all input taxids are deleted or "unfound" (#22)
+- Bug causing `pytaxonkit.name` to fail on empty inputs (#26)
+
+
 ## [0.7.2] 2021-01-27
 
 ### Added
@@ -10,9 +25,6 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Support for new `prefix` related flags (#6)
 - Use new `--show-lineage-ranks` to create new `FullLineageRanks` column in `lineage()` output (#8)
 
-### Fixed
-- Bug with empty inputs (#19)
-
 
 ## [0.6.1] 2020-10-30
 

Makefile

@@ -11,14 +11,19 @@ test4:
 	COLUMNS=150 pytest -n 4 --cov=pytaxonkit --doctest-modules pytaxonkit.py conftest.py
 
 
-## style:    check code style against PEP8
+## style:    check code style
 style:
-	pycodestyle --max-line-length=99 pytaxonkit.py
+	black --line-length=99 --check pytaxonkit.py setup.py
+
+
+## format:   autoformat Python code
+format:
+	black --line-length=99 pytaxonkit.py setup.py
 
 
 ## devenv:   set up a development environment
 devenv:
-	conda install -y pycodestyle pytest pytest-cov
+	conda install -y black==22.6.0 pytest pytest-cov
 	pip install -e .
 	echo 'make style' >> .git/hooks/pre-commit
 	chmod 755 .git/hooks/pre-commit

README.md

@@ -24,8 +24,9 @@ Execute `help(pytaxonkit.name2taxid)` (and so on) from the Python interpreter fo
 
 > **NOTES**
 > - The `reformat` operation is automatically run by `pytaxonkit.lineage` and cannot be invoked independently.
-> - The `taxid-changelog` operation is not supported.
 > - The `genautocomplete` operation is specific to the shell and is not supported.
+> - Several other operations are not supported, including `cami-filter`, `create-taxdump`, `profile2cami`, and `taxid-changelog`.
+> - The `pytaxonkit.__version__` variable refers to the version number of the Python bindings, while the `pytaxonkit.__taxonkitversion__` variable corresponds to the version of the installed TaxonKit program. These version numbers are not necessarily equal.
 
 ### name2taxid
 
@@ -95,7 +96,6 @@ BasicTaxon(taxid=9904, rank='species', name='Bos gaurus')
 >>> import pytaxonkit
 >>> taxids = [131567, 2759, 33154, 33208, 6072, 33213, 33317, 1206794, 88770, 6656, 197563, 197562, 6960, 50557, 85512, 7496, 33340, 33392, 85604, 7088]
 >>> result = pytaxonkit.filter(taxids, equal_to='phylum', higher_than='phylum')
->>> pytaxonkit.name(result)
 >>> pytaxonkit.name(result)
    TaxID        Name
 0   2759   Eukaryota

environment.yaml

@@ -4,9 +4,9 @@ channels:
  - conda-forge
  - defaults
 dependencies:
+ - black==22.6.0
  - pandas>=1.0
  - python>=3.6
- - pycodestyle>=2.5
  - pytest>=5.4
  - pytest-cov>=2.8
  - pytest-xdist>=1.31